Publications of the CSL group2019
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PhD Thesis. The emergence of biofilms. Supervised by P. M. A. Sloot.
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Article. Semi-intrusive multiscale metamodelling uncertainty quantification with application to a model of in-stent restenosis. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences 377(2142), 2018154.
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Article. Red blood cell and platelet diffusivity and margination in the presence of cross-stream gradients in blood flows. Physics of Fluids 31(3), 031903.
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Article. Patterns for High Performance Multiscale Computing. Future Generation Computer Systems 91, pp. 335-346.
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Proceedings. Optimizing Parallel Performance of the Cell Based Blood Flow Simulation Software HemoCell. In: Computational Science – ICCS 2019. ISBN 9783030227449. 11538, pp. 537-547.
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Article. Multiple Aneurysms AnaTomy CHallenge 2018 (MATCH)—phase II: rupture risk assessment. International Journal of Computer Assisted Radiology and Surgery .
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Article. Modeling the effect of high calorie diet on the interplay between adipose tissue, inflammation and diabetes. Computational and Mathematical Methods in Medicine 2019, 7525834.
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Article. Low and variable pH decreases recruitment efficiency in populations of a temperate coral naturally present at CO2 vent. Limnology and Oceanography 64(3), pp. 1059-1069.
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Article. Image Based Classification of Slums, Built-Up and Non-Built-Up Areas in Kalyan and Bangalore, India. European Journal of Remote Sensing 52(S1), pp. 40-61.
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Article. Boolean network modeling of β-cell apoptosis and insulin resistance in type 2 diabetes mellitus. BMC Systems Biology 13(36).
2018
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Proceedings. Vulnerability Of Charging Infrastructure, A Novel Approach For Improving Charging Station Deployment. In: Proceedings of 7th Transport Research Arena TRA 2018, April 16.
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Article. Urgent computing for decision support in critical situations. Future Generation Computer Systems 79(1), pp. 111-113.
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Proceedings. Understanding Malaria Induced Red Blood Cell Deformation Using Data-Driven Lattice Boltzmann Simulations. In: Computational Science – ICCS 2018. ISBN 9783319936987. pp. 392-403.
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Article. Uncertainty Quantification of a Multiscale Model for In-Stent Restenosis. Cardiovascular Engineering and Technology 9(4), pp. 761-774.
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PhD Thesis. Toward reverse engineering spatiotemporal gene regulatory networks of Nematostella vectensis. ISBN 9789402810110. Supervised by P. M. A. Sloot and J. A. Kaandorp.
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Article. The art of computational science: Bridging gaps – forming alloys. Journal of Computational Science 26, pp. 190-192.
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Article. System dynamics of human body thermal regulation in outdoor environments. Building and Environment 143, pp. 760-769.
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Article. Survey-based socio-economic data from slums in Bangalore, India. Scientific Data 5, 170200.
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Article. Supplemented alkaline phosphatase supports the immune response in patients undergoing cardiac surgery: Clinical and computational evidence. Frontiers in Immunology 9, 2342.
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Article. Spatial segregation, inequality, and opportunity bias in the slums of Bengaluru. Cities : The International Journal of Urban Policy and Planning 74, pp. 269-276.
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Article. Quantification of complex modular architecture in plants. New Phytologist 218(2), pp. 859-872.
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PhD Thesis. Patterns for multiscale computing. ISBN 9789463234092. Supervised by P. M. A. Sloot and A. G. Hoekstra.
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Article. Numerical investigation of the effects of red blood cell cytoplasmic viscosity contrasts on single cell and bulk transport behaviour. Applied Sciences 8(9), 1616.
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Article. Morphogenesis in Robot Swarms. Science Robotics 3(25), eaau9178.
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Article. Mesoscopic Energy Minimization Drives Pseudomonas aeruginosa Biofilm Morphologies and Consequent Stratification of Antibiotic Activity Based on Cell Metabolism. Antimicrobial Agents and Chemotherapy 62(4), e02544-17.
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Article. Load balancing of parallel cell-based blood flow simulations. Journal of Computational Science 24, pp. 1-7.
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Article. Liquidity risk in derivatives valuation: an improved credit proxy method. Quantitative Finance 18(3), pp. 467-481.
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Report. IvI Education vision.
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Article. Information processing features can detect behavioral regimes of dynamical systems. Complexity 2018, 6047846.
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Article. Incorporating Contagion in Portfolio Credit Risk Models Using Network Theory. Complexity 2018, 6076173.
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Article. High-throughput method for extracting and visualizing the spatial gene expressions from in situ hybridization images: A case study of the early development of the sea anemone Nematostella vectensis. Gene expression patterns : GEP 27, pp. 36-45.
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Article. Financial statement networks: an application of network theory in audit. The Journal of Network Theory in Finance 4(4), pp. 59-85.
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Proceedings. Evolutionary Game Theory Can Explain the Choice Between Apoptotic and Necrotic Pathways in Neutrophils. In: Proceedings 2018 IEEE International Conference on Bioinformatics and Biomedicine. ISBN 9781538654880, 9781538654873. pp. 1401-1405.
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Article. Epigenome-associated phenotypic acclimatization to ocean acidification in a reef-building coral. Sciences advances 4(6), eaar8028.
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Article. Directed nucleation and growth by balancing local supersaturation and substrate/nucleus lattice mismatch. Proceedings of the National Academy of Sciences of the United States of America 115(14), pp. 3575-3580.
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Article. Combined Lattice–Boltzmann and rigid-body method for simulations of shear-thickening dense suspensions of hard particles. Computers & fluids 172, pp. 474-482.
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Article. Cell-resolved blood flow simulations of saccular aneurysms: effects of pulsatility and aspect ratio. Journal of the Royal Society Interface 15(146), 20180485.
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Article. Categorical and Geographical Separation in Science. Scientific Reports 8, 8253.
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Article. Analysis of publication activity of computational science society in 2001–2017 using topic modelling and graph theory. Journal of Computational Science 26, pp. 193-204.
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Article. A study on the dynamics of temporary HIV treatment to assess the controversial outcomes of clinical trials: An in-silico approach. PLoS ONE 13(7), e0200892.
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Article. A new hypothesis on the role of vessel topology in cerebral aneurysm initiation. Computers in Biology and Medicine 103, pp. 244-251.
2017
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Article. eHealth in the future of medications management: personalisation, monitoring and adherence. BMC Medicine 15, 73.
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Article. Uncertainty quantification and sensitivity analysis applied to the wind wave model SWAN. Environmental Modelling & Software 95, pp. 344-357.
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Article. The study of the influence of obstacles on crowd dynamics. Procedia Computer Science 108, pp. 215-224.
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Article. The effect of allometric scaling in coral thermal microenvironments. PLoS ONE 12(10), e0184214.
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Article. The Art of Computational Science, Bridging Gaps - Forming Alloys. Procedia Computer Science 108, pp. 1-6.
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Article. The Art of Computational Science, Bridging Gaps - Forming Alloys. Procedia Computer Science 108, pp. 1-2.
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Article. Scatter Search Applied to the Inference of a Development Gene Network. Computation 5(2), 22.
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Article. Revisiting the use of the immersed-boundary lattice-Boltzmann method for simulations of suspended particles. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 96(1), 013302.
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Article. Relaxing Synchronization in Parallel Agent-Based Road Traffic Simulation. ACM Transactions on Modeling and Computer Simulation 27(2), 14.
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Article. Quantitative morphological analysis of 2D images of complex-shaped branching biological growth forms: the example of branching thalli of liverworts. BMC Research Notes 10(1), 103.
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Article. Quantifying Synergistic Information Using Intermediate Stochastic Variables. Entropy 19(2), 85.
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PhD Thesis. Phase transitions in complex systems. Supervised by P. M. A. Sloot, A. G. Hoekstra, and R. Quax.
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Article. Novel approach to investigation of semiconductor MOCVD by microreactor technology. Journal of Physics. Conference Series 917, 032011.
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Article. Multiscale computing in the exascale era. Journal of Computational Science 22, pp. 15-25.
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Article. Multiscale Modelling and Simulation, 14th International Workshop. Procedia Computer Science 108, pp. 1811-1812.
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Chapter. More likely we would be ritually slaughtered. In: 43 Visions for Complexity. ISBN 9789813206854. pp. 65-66.
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Article. Models of Pedestrian Adaptive Behaviour in Hot Outdoor Public Spaces. Procedia Computer Science 108, pp. 185-194.
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Article. Modelling the impact of household life cycle on slums in Bangalore. Computers, Environment and Urban Systems 64, pp. 275-287.
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Article. Modelling the distance impedance of protest attendance. Physica A : Statistical Mechanics and its Applications 468, pp. 171-182.
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Book. International Conference on Computational Science, ICCS 2017.
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Article. Hemocell: a high-performance microscopic cellular library. Procedia Computer Science 108, pp. 159-165.
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Article. Efficient Estimation of Sensitivities for Counterparty Credit Risk with the Finite Difference Monte Carlo Method. Journal of Computational Finance 21(1), pp. 83-113.
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Article. Design and evaluation of a data-driven scenario generation framework for game-based training. IEEE Transactions on Computational Intelligence and AI in Games 9(3), pp. 213-226.
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Article. Data through the Computational Lens. Journal of Computational Science 20, pp. 81-84.
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Article. Cellular Level In-silico Modeling of Blood Rheology with An Improved Material Model for Red Blood Cells. Frontiers in Physiology 8, 563.
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Article. Automatic model construction for the behavior of human crowds. Applied Soft Computing 56, pp. 368-378.
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Article. Anomaly detection in earth dam and levee passive seismic data using support vector machines and automatic feature selection. Journal of Computational Science 20, pp. 143-153.
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Proceedings. Anomaly detection in earth dam and levee passive seismic data using multivariate Gaussian. In: ICMLA 2017 : 16th IEEE International Conference on Machine Learning and Applications. ISBN 9781538614174, 9781538614181. pp. 685-690.
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Article. Anomaly Detection in Clinical Data of Patients Undergoing Heart Surgery. Procedia Computer Science 108, pp. 99-108.
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Article. Analysis of Computational Science Papers from ICCS 2001-2016 using Topic Modeling and Graph Theory. Procedia Computer Science 108, pp. 7-17.
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Article. A physical description of the adhesion and aggregation of platelets. Royal Society Open Science 4, 170219.
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Article. A novel technique to combine and analyse spatial and temporal expression datasets: A case study with the sea anemone Nematostella vectensis to identify potential gene interactions. Developmental Biology 428(1), pp. 204-214.
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Article. A Comparison of Fully-Coupled 3D In-Stent Restenosis Simulations to In-vivo Data. Frontiers in Physiology 8, 284.
2016
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Article. Towards the virtual artery: a multiscale model for vascular physiology at the physics–chemistry–biology interface. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences 374(2080), 20160146.
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Article. The influence of memory on indoor environment exploration: A numerical study. Behavior Research Methods 48(2), pp. 621-639.
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Chapter. Systems Biology and Health Systems Complexity. In: The Digital Patient. ISBN 9781118952788. pp. 73-84.
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PhD Thesis. Spatial gene expression quantification in changing morphologies. Supervised by P. M. A. Sloot and J. A. Kaandorp.
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Article. Smile and Default: The Role of Stochastic Volatility and Interest Rates in Counterparty Credit Risk. Quantitative Finance 16(11), pp. 1725-1740.
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Article. Simulating an Impact of Road Network Improvements on the Performance of Transportation Systems under Critical Load: Agent-based Approach. Procedia Computer Science 101, pp. 253-261.
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Article. Scaling of shear-induced diffusion and clustering in a blood-like suspension. Europhysics Letters 114(1), 14002.
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Proceedings. Reproducibility of Two Innate Immune System Models. In: Digital Transformation and Global Society. ISBN 9783319497006. pp. 501-514.
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Article. Nonparametric estimation of Fisher information from real data. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 93(2), 023301.
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Article. Multiscale modelling and simulation, 13th international workshop. Procedia Computer Science 80, pp. 1242-1243.
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Article. Luminescence and density banding patterns in massive Porites corals around the Thai-Malay Peninsula, Southeast Asia. Limnology and Oceanography 61(6), pp. 2003-2026.
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Book. International Conference on Computational Science 2016, ICCS 2016.
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Article. Information geometric analysis of phase transitions in complex patterns: the case of the Gray-Scott reaction-diffusion model. Journal of Statistical Mechanics : Theory and Experiment 2016(4), 043301.
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Article. Immune System Model Calibration by Genetic Algorithm. Procedia Computer Science 101, pp. 161-171.
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Chapter. From Molecules to Morphologies, a Multiscale Modeling Approach to Unravel the Complex System of Coral Calcification. In: The Cnidaria, Past, Present and Future. ISBN 9783319313054. pp. 223-236.
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Article. From MDMA to Lady Gaga. Procedia Computer Science 101, pp. 96-106.
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Article. Efficient computation of exposure profiles on real-world and risk-neutral scenarios for Bermudan swaptions. Journal of Computational Finance 20(1), pp. 139-172.
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PhD Thesis. Efficient PDE based numerical estimation of credit and liquidity risk measures for realistic derivative portfolios. ISBN 978-94-028-0408-9. Supervised by P. M. A. Sloot and B. D. Kandhai.
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Article. Development and simulation of microfluidic Wheatstone bridge for high-precision sensor. Journal of Physics. Conference Series 738, 012071.
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PhD Thesis. Detecting and disrupting criminal networks. ISBN 978-90-77595-41-1. Supervised by A. G. Hoekstra and Z. J. M. H. Geradts.
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Article. Data-driven Travel Demand Modelling and Agent-based Traffic Simulation in Amsterdam Urban Area. Procedia Computer Science 80, pp. 2030-2041.
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Article. Data through the Computational Lens, Preface for ICCS 2016. Procedia Computer Science 80, pp. 1-7.
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Article. Crack detection in earth dam and levee passive seismic data using support vector machines. Procedia Computer Science 80, pp. 577-586.
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Article. Corrigendum to “The discrete dipole approximation: An overview and recent developments” [J. Quant. Spectrosc. Radiat. Transfer 106 (2007) 558–589]. Journal of Quantitative Spectroscopy & Radiative Transfer 171, pp. 82-83.
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Article. Corrigendum to “Experience of using FEM for real-time flood early warning systems: Monitoring and modelling Boston levee instability”. Journal of Computational Science 16, pp. 225-226.
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Article. Computer Simulation Approach in Development of Propane-air Combustor Microreactor. Procedia Computer Science 101, pp. 76-85.